IndexError: tuple index out of range

[Sendong98]

Hi
I'm trying to do some imputation checks by masking the genotype data and it worked well with the original file but always get errors when I use the file that I added random 9(missing value) into the genotype file:
File "/home1/p314480/.local/lib/python3.10/site-packages/alphaimpute2/Imputation/BurrowsWheelerLibrary.py", line 65, in setup_library
bw_loci = np.array(range(self.haplotypes.shape[1]), dtype = np.int64)
IndexError: tuple index out of range
How could I solve this problem? Thank you!

[gregorgorjanc]

@Sendong98 this is odd. Can you provide a reproducible example?

[Sendong98]

Of course, here's an example for the Alphaimpute example genotype file: I added random 9 and got the error during imputation.
original file (genotype and pedigree data )downloaded from https://github.com/AlphaGenes/AlphaImpute2/tree/main/example masked 10% genotype data generated by adding random missing value
command used: AlphaImpute2 -genotypes genotypes_mask10.txt -pedigree pedigree.txt -out test -writekey genotypes -onlykeyed -cycles 10 -maxthreads 12
genotypes_mask10.txt
genotypes_original.txt
pedigree.txt

[yqiqichen]

I can reproduce the error on my end. And I will try to identify the cause of the error.

[yqiqichen]

I have found out the cause of the error. It is because if there are a lot of '9' in 'genotypes.txt' file, 'self.haplotypes' of function 'setup_library' in file 'BurrowsWheelerLibrary.py' has shape (0,), but we use self.haplotypes.shape[1], which does not exist and leads to the error. I have now modified the function 'setup_library'.